核糖体分型的分子遗传基础。
Molecular genetic basis of ribotyping.
作者信息
Bouchet Valérie, Huot Heather, Goldstein Richard
机构信息
Section of Molecular Genetics, Division of Pediatric Infectious Diseases, The Maxwell Finland Laboratory for Infectious Diseases, Boston University School of Medicine, Boston Medical Center, BioSquare-III, Boston, MA 02118, USA.
出版信息
Clin Microbiol Rev. 2008 Apr;21(2):262-73, table of contents. doi: 10.1128/CMR.00026-07.
Abstract
Nearly 2,000 ribotyping-based studies exist, ranging from epidemiology to phylogeny and taxonomy. None precisely reveals the molecular genetic basis, with many incorrectly attributing detected polymorphisms to rRNA gene sequences. Based on in silico genomics, we demonstrate that ribotype polymorphisms result from sequence variability in neutral housekeeping genes flanking rRNA operons, with rRNA gene sequences serving solely as conserved, flank-linked tags. We also reveal that from such an informatics perspective, it is readily feasible a priori to design an interpretable ribotyping scheme for a genomically sequenced microbial species, and we discuss limitations to the basic restriction fragment length polymorphism-based method as well as alternate PCR ribotyping-based schemes.
摘要
目前已有近2000项基于核糖体分型的研究，涵盖从流行病学到系统发育和分类学等领域。但没有一项研究能精确揭示其分子遗传基础，许多研究将检测到的多态性错误地归因于rRNA基因序列。基于计算机基因组学，我们证明核糖体分型多态性是由rRNA操纵子侧翼中性管家基因的序列变异性导致的，rRNA基因序列仅作为保守的、侧翼连接的标签。我们还揭示，从这样的信息学角度来看，事先为基因组已测序的微生物物种设计一个可解释的核糖体分型方案是完全可行的，并且我们讨论了基于基本限制性片段长度多态性方法以及基于PCR核糖体分型替代方案的局限性。
相似文献
1
Molecular genetic basis of ribotyping.
Clin Microbiol Rev. 2008 Apr;21(2):262-73, table of contents. doi: 10.1128/CMR.00026-07.
2
Molecular characterization of Streptococcus equi subspecies equi isolated from an Ethiopian camel by ribotyping and PCR-ribotyping.
New Microbiol. 1999 Oct;22(4):383-7.
3
Source of variation detected in ribotyping patterns of Haemophilus influenzae: comparison of traditional ribotyping, PCR-ribotyping and rDNA restriction analysis.
J Med Microbiol. 1997 Sep;46(9):763-72. doi: 10.1099/00222615-46-9-763.
4
DNA-based classification and sequence heterogeneities in the 16S rRNA genes of Lactobacillus casei/paracasei and related species.
Syst Appl Microbiol. 2005 Jul;28(5):430-41. doi: 10.1016/j.syapm.2005.02.011.
5
Lack of polymorphism within the rRNA operons of group A streptococci.
Mol Gen Genet. 1997 Jun;255(1):125-30. doi: 10.1007/s004380050480.
6
Long PCR-ribotyping of nontypeable Haemophilus influenzae.
J Clin Microbiol. 1995 May;33(5):1192-5. doi: 10.1128/jcm.33.5.1192-1195.1995.
7
New opportunities for improved ribotyping of C. difficile clinical isolates by exploring their genomes.
J Microbiol Methods. 2013 Jun;93(3):257-72. doi: 10.1016/j.mimet.2013.02.013. Epub 2013 Mar 29.
8
Molecular epidemiology of Pseudomonas cepacia determined by polymerase chain reaction ribotyping.
J Clin Microbiol. 1992 Aug;30(8):2084-7. doi: 10.1128/jcm.30.8.2084-2087.1992.
9
Ribotyping, biotyping and capsular typing of Haemophilus influenzae strains isolated from patients in Campinas, southeast Brazil.
Braz J Infect Dis. 2008 Oct;12(5):430-7. doi: 10.1590/s1413-86702008000500015.
10
Reprint of New opportunities for improved ribotyping of C. difficile clinical isolates by exploring their genomes.
J Microbiol Methods. 2013 Dec;95(3):425-40. doi: 10.1016/j.mimet.2013.09.009. Epub 2013 Sep 16.
引用本文的文献
1
Paternal microbiota manipulation influences offspring microbial colonization and development in a sex role-reversed pipefish.
Sci Rep. 2025 Aug 22;15(1):30911. doi: 10.1038/s41598-025-16222-y.
2
Molecular epidemiology and molecular typing methods of : An updated review.
Saudi Med J. 2024 May;45(5):458-467. doi: 10.15537/smj.2024.45.5.20230886.
3
Comparison of genotyping methods and toxin gene profiles of Staphylococcus aureus isolates from clinical specimens.
Genet Mol Biol. 2023 Dec 22;46(4):e20220321. doi: 10.1590/1678-4685-GMB-2022-0321. eCollection 2023.
4
Comparison of Automated Ribotyping, Typing, and MLST in 108 Clinical Isolates of from Orthopedic Infections.
Int J Mol Sci. 2022 Jan 31;23(3):1660. doi: 10.3390/ijms23031660.
5
Defining the black box: a narrative review of factors associated with adverse outcomes from severe infection.
Therap Adv Gastroenterol. 2021 Oct 8;14:17562848211048127. doi: 10.1177/17562848211048127. eCollection 2021.
6
Insights Into Subspecies Discrimination Potentiality From Bacteria MALDI-TOF Mass Spectra by Using Data Mining and Diversity Studies.
Front Microbiol. 2020 Aug 13;11:1931. doi: 10.3389/fmicb.2020.01931. eCollection 2020.
7
Advances in Chemical and Biological Methods to Identify Microorganisms-From Past to Present.
Microorganisms. 2019 May 13;7(5):130. doi: 10.3390/microorganisms7050130.
8
Methods for Studying Gut Microbiota: A Primer for Physicians.
J Clin Exp Hepatol. 2019 Jan-Feb;9(1):62-73. doi: 10.1016/j.jceh.2018.04.016. Epub 2018 May 4.
9
Frequency of enterotoxins, toxic shock syndrome toxin-1, and biofilm formation genes in Staphylococcus aureus isolates from cows with mastitis in the Northeast of Brazil.
Trop Anim Health Prod. 2018 Jun;50(5):1089-1097. doi: 10.1007/s11250-018-1534-6. Epub 2018 Feb 10.
10
Genomic analysis of endemic clones of toxigenic and non-toxigenic Corynebacterium diphtheriae in Belarus during and after the major epidemic in 1990s.
BMC Genomics. 2017 Nov 13;18(1):873. doi: 10.1186/s12864-017-4276-3.
本文引用的文献
1
Strain characteristics of Streptococcus pneumoniae carriage and invasive disease isolates during a cluster-randomized clinical trial of the 7-valent pneumococcal conjugate vaccine.
J Infect Dis. 2007 Oct 15;196(8):1221-7. doi: 10.1086/521831. Epub 2007 Sep 17.
2
Prevalence of toxin A-nonproducing/toxin-B-producing Clostridium difficile in the Tsukuba-Tsuchiura district, Japan.
J Infect Chemother. 2007 Feb;13(1):35-8. doi: 10.1007/s10156-006-0494-3. Epub 2007 Feb 26.
3
Typing and subtyping of Clostridium difficile isolates by using multiple-locus variable-number tandem-repeat analysis.
J Clin Microbiol. 2007 Mar;45(3):1024-8. doi: 10.1128/JCM.02023-06. Epub 2006 Dec 13.
4
The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome.
Nat Genet. 2006 Jul;38(7):779-86. doi: 10.1038/ng1830. Epub 2006 Jun 25.
5
Comparative genome analysis of Vibrio vulnificus, a marine pathogen.
Genome Res. 2003 Dec;13(12):2577-87. doi: 10.1101/gr.1295503.
6
Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes.
Appl Environ Microbiol. 2003 Sep;69(9):5512-8. doi: 10.1128/AEM.69.9.5512-5518.2003.
7
Host-derived sialic acid is incorporated into Haemophilus influenzae lipopolysaccharide and is a major virulence factor in experimental otitis media.
Proc Natl Acad Sci U S A. 2003 Jul 22;100(15):8898-903. doi: 10.1073/pnas.1432026100. Epub 2003 Jul 10.
8
Conservation of the mosaic structure of the four internal transcribed spacers and localisation of the rrn operons on the Streptococcus pneumoniae genome.
FEMS Microbiol Lett. 2003 Jun 27;223(2):245-52. doi: 10.1016/S0378-1097(03)00376-8.
9
High rates of recombination in otitis media isolates of non-typeable Haemophilus influenzae.
Infect Genet Evol. 2003 May;3(1):57-66. doi: 10.1016/s1567-1348(02)00152-1.
10
Ribotyping of Clostridium perfringens from industrially produced ground meat.
Lett Appl Microbiol. 2002;34(4):238-43. doi: 10.1046/j.1472-765x.2002.01100.x.
Zotero 插件